I don't like the Bosch returning bit much really.
That stuff about the uprising and Khonsu dying is good, though. Make sure there is a very good reason for the Vasudan rebellion, maybe a reason that would convince a few Terrans to join in too.
Maaaaybe... you could choose whether or not to join the rebellion at some point. This could be done in two ways... either an SOC screen or a mission event. If, for example, you fire on a friendly ship in a particular mission after being asked to do so by an enemy ship, you could change the path of the mission tree. (There will be a tree, right?) In that mission all friendly IFFs would become hostile and vice versa.